β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (ChIP-seq)

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrate that this differentiated state is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the ACC epigenome. On chromatin, β-catenin binds master adrenal transcription factor SF1 and hijacks the adrenocortical super-enhancer landscape to maintain differentiation. Off chromatin, β-catenin binds histone methyltransferase EZH2, which is redistributed by the CIMP-high DNA methylation signature. SF1/β-catenin and EZH2/β-catenin complexes exist in normal adrenals and are selected for through all phases of ACC evolution. EZH2 inhibition in CIMP-high ACC favors EZH2/β-catenin assembly and purges SF1/β-catenin from chromatin, erasing differentiation and restraining cancer growth in vitro and in vivo. Our studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities. Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline) or EZH2 inhibitor EPZ-6438 (EZH2i) to evaluate the impact of EZH2 inhibition on the ACC epigenome. At endpoint, cells were harvested for ChIP-seq using antibodies against the following epitopes: H3K27ac, H3K27me3, EZH2, β-catenin, steroidogenic factor 1 (SF1). We used Drosophila melanogaster chromatin as a spike-in control to enable quantitative comparisons across ChIP-seq samples.